GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 206139 DVU0714 branched-chain amino acid ABC transporter, permease protein

Query= uniprot:A0A165KER0
         (358 letters)



>MicrobesOnline__882:206139
          Length = 317

 Score =  210 bits (534), Expect = 5e-59
 Identities = 132/346 (38%), Positives = 193/346 (55%), Gaps = 47/346 (13%)

Query: 1   MKNTKTNWIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGY 60
           M + K ++   AV + VLPL L  +   W  +     LY +LAL LN+++G AGL  +G+
Sbjct: 1   MISRKASYAGLAVLIAVLPLFLDPY---WTDVCVSIGLYAVLALSLNLILGQAGLFHMGH 57

Query: 61  VAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPT 120
            AFYAVGAY  A++ + +                H  +   +PVA LLAA F  ++  P 
Sbjct: 58  AAFYAVGAYTAAILNTVY----------------HVPVLWTMPVAGLLAALFALVVARPI 101

Query: 121 LKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFG 180
           + LRGDYL IVT+G  EI+RI L N  +   +T G  G        +FG+    R  +FG
Sbjct: 102 IHLRGDYLLIVTIGIVEIVRIALIN--NVFGITGGANG--------IFGIS---RPMLFG 148

Query: 181 FDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLA 240
           + I+    +YYL    V +S+++  RL+ SR GRA   I+ED++AA+  G++T   KL A
Sbjct: 149 YKISKPIQFYYLIWTWVAISILLFRRLECSRFGRALNYIKEDDVAAEGSGVDTAYYKLAA 208

Query: 241 FGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSAL 300
           F +GA + G++G  + A    +SPESFS  ESV++ A+V+LGG G   GV+LGA LL  L
Sbjct: 209 FVLGALWAGMTGTFYAAKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGL 267

Query: 301 PEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346
           PE+ R              D A  R L+  LAM+++M+ RP+G+ P
Sbjct: 268 PELFR--------------DFASARMLIFGLAMVVMMIFRPQGMLP 299


Lambda     K      H
   0.328    0.144    0.430 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 294
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 317
Length adjustment: 28
Effective length of query: 330
Effective length of database: 289
Effective search space:    95370
Effective search space used:    95370
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory